picard.sam.SamErrorMetric.IndelErrorCalculator Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2019 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.sam.SamErrorMetric;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.reference.SamLocusAndReferenceIterator;
import htsjdk.samtools.util.AbstractRecordAndOffset;
import htsjdk.samtools.util.SamLocusIterator;
/**
* A calculator that estimates the error rate of the bases it observes for indels only.
*/
public class IndelErrorCalculator extends BaseErrorCalculator {
/**
* Total number of inserts
*/
protected long nInsertions;
/**
* Total number of inserted bases
*/
protected long nInsertedBases;
/**
* Total number of deletions
*/
protected long nDeletions;
/**
* Total number of deleted bases
*/
protected long nDeletedBases;
@Override
public void addBase(final SamLocusIterator.RecordAndOffset recordAndOffset, final SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef) {
super.addBase(recordAndOffset, locusAndRef);
if (recordAndOffset.getAlignmentType() == AbstractRecordAndOffset.AlignmentType.Insertion) {
nInsertions++;
CigarElement cigarElement = ReadBaseStratification.getIndelElement(recordAndOffset);
if (cigarElement != null) {
nInsertedBases += cigarElement.getLength();
}
} else if (recordAndOffset.getAlignmentType() == AbstractRecordAndOffset.AlignmentType.Deletion) {
nDeletions++;
CigarElement cigarElement = ReadBaseStratification.getIndelElement(recordAndOffset);
if (cigarElement != null) {
nDeletedBases += cigarElement.getLength();
}
}
}
/**
* The suffix that pertains to the implementation of aggregation
**/
@Override
public String getSuffix() {
return "indel_error";
}
/**
* Returns the metric generated by the observed loci
**/
@Override
public IndelErrorMetric getMetric() {
return new IndelErrorMetric("", nBases, nInsertions, nInsertedBases, nDeletions, nDeletedBases);
}
}